Data with paper "Size Laws and Division Ring Dynamics in Filamentous Escherichia coli cells"

See also the other Zenodo record: https://zenodo.org/records/11401470

Data files related to manuscript:

Wehrens M, Ershov D, Rozendaal R, Walker N, Schultz D, Kishony R, Levin PA, Tans SJ (2018). “Size Laws and Division Ring Dynamics in Filamentous Escherichia coli cells”. Current Biology.

https://doi.org/10.1016/j.cub.2018.02.006

Currently, single cell experimental time trace data for figures 1, 2 and 4 is added. Additional data will follow.

Scripts are available at:

https://github.com/TansLab/Tans_filamentation

And you will also need the additional scripts from the repositories:

https://github.com/TansLab/Common_libraries

https://github.com/TansLab/Tans_Schnitzcells

Script that generates figures:

https://github.com/TansLab/Tans_filamentation/blob/master/ershovwehrensallfigures.m

And more specifically, data is loaded, (partially analyzed,) and plotted here:

https://github.com/TansLab/Tans_filamentation/blob/master/script20160429_filamentRecoveryDivisionRatioss.m

Description of the .mat files

These .mat files contain the lineage information, which were used to generate figures 1 and 2.

Each row corresponds to a cell from birth to division.

Most important fields are:

P is its parent cell (number referring to the row of the table).

E is the daughter cell after this cell divides

D is the other daughter cell after this cell divides

frame_nrs is in which frame this cell lived

areapx is its area in pixels

Different methods were used to determine the bacterias length. For the tetracycline experiments, often the field “length_fitNew” was used, which is a higher order polynomial fitted through the bacterium. For the other stress conditions, mostly the field “length_skeleton” was used, which is the length of the skeleton of the bacteria, extrapolated until it reaches the bacterial edge (this was done because in those experiments, these bacteria often had weird shapes that couldn’t be fitted by polynomials).

The growth rate of the bacteria is determined by fitting an exponential curve through length information of multiple frames. Given the fluctuation of growth rates, sometimes bacteria grow relatively slow over a certain amount of frames, or relatively fast. Therefor, sometimes the fit is done using more or less frames. The growth rate information can be found in e.g. the parameters 'muP15_fitNew_all','muP9_skeleton_all','muP5_skeleton_all', where mu refers to growth rate, PX indicates X frames around the frame of interest were used for the fit, and fitNew_all or skeleton_all refers respectively to which length parameter was used for the fit.

Note that birth sizes and interdivision times, as wel as added length, can be calculated from the above parameters using the data structure. (See also applicable scripts.)

The data also contains more fields with information about length and size, and also fields for fluorescence data. The latter is not really applicable here. 

See also the methods section of the paper for more information.

INFORMATION ABOUT THE DATA

Files for the SulA condition:

Data file

Switch time from stress to stress-free condition (min)

\2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTG\pos1crop\data\pos1crop-Schnitz.mat

0

\2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTG\pos2crop\data\pos2crop-Schnitz.mat

0

\2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTG\pos3crop\data\pos3crop-Schnitz.mat

0

\2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTG\pos4crop\data\pos4crop-Schnitz.mat

0

\2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTG\pos7crop\data\pos7crop-Schnitz.mat

0

If switch time is zero, recording started at the switch time.

For the temperature condition

Data file

Switch time from stress to stress-free condition (min)

2016-03-23_FilaRecovery_asc777_42C\pos4crop\data\pos4crop-Schnitz.mat

450

2016-04-07_FilaRecovery_asc777\pos2crop\data\pos2crop-Schnitz.mat

329

Delta min tetracycline condition

Data file

Switch time from stress to stress-free condition (min)

2017-09-22_FilaRecovery_asc1035_DeltaMinCDE\pos1cropb\data\pos1cropb-Schnitz.mat

5

2017-09-22_FilaRecovery_asc1035_DeltaMinCDE\pos2cropa\data\pos2cropa-Schnitz.mat

5

2017-09-22_FilaRecovery_asc1035_DeltaMinCDE\pos2cropb\data\pos2cropb-Schnitz.mat

5

2017-09-22_FilaRecovery_asc1035_DeltaMinCDE\pos2cropc\data\pos2cropc-Schnitz.mat

5

2017-09-22_FilaRecovery_asc1035_DeltaMinCDE\pos3cropa\data\pos3cropa-Schnitz.mat

5

Tetracycline data

Only data sets 1 to 5 where used here

Data file

Switch time from stress to stress-free condition (min)

F schijf AmolfBackup_3april2014\USE_DIV\1uM_pos3_long.mat

890.9800 

F schijf AmolfBackup_3april2014\USE_DIV\1uM_pos4.mat

404.7500        

F schijf AmolfBackup_3april2014\USE_DIV\1uM_pos4_long.mat

0 

F schijf AmolfBackup_3april2014\USE_DIV\1uM_pos5.mat

529.7600 

F schijf AmolfBackup_3april2014\USE_DIV\1uM_pos5_long.mat

0

F schijf AmolfBackup_3april2014\USE_DIV\2uM_pos2.mat

NA

F schijf AmolfBackup_3april2014\USE_DIV\2uM_pos4.mat

NA

F schijf AmolfBackup_3april2014\USE_DIV\2uM_pos6.mat

NA

F schijf AmolfBackup_3april2014\USE_DIV\10uM_pos1.mat

NA

F schijf AmolfBackup_3april2014\USE_DIV\10uM_pos3.mat

NA

F schijf AmolfBackup_3april2014\USE_DIV\10uM_pos6_long.mat

NA

Tetracycline data 2 (redundant with above)

Data file

Switch time from stress to stress-free condition (min)

2013-12-09\pos3crop\data\pos3crop-Schnitz.mat

890.9800 

2013-09-24\pos4crop\data\pos4crop-Schnitz.mat

404.7500        

2013-12-16\pos4crop\data\pos4crop-Schnitz.mat

0 

2013-09-24\pos5crop\data\pos5crop-Schnitz.mat

529.7600 

2013-12-16\pos5crop\data\pos5crop-Schnitz.mat

0

另请参阅另一项Zenodo记录：https://zenodo.org/records/11401470

与该论文相关的数据文件：

Wehrens M、Ershov D、Rozendaal R、Walker N、Schultz D、Kishony R、Levin PA、Tans SJ（2018）。《丝状大肠杆菌（Escherichia coli）细胞的尺寸规律与分裂环动力学》，发表于《当代生物学》（Current Biology）。
https://doi.org/10.1016/j.cub.2018.02.006

目前已补充用于制作图1、图2与图4的单细胞实验时间轨迹数据，后续将追加更多数据集。

相关脚本可从以下仓库获取：
https://github.com/TansLab/Tans_filamentation

此外还需从以下仓库获取配套脚本：
https://github.com/TansLab/Common_libraries
https://github.com/TansLab/Tans_Schnitzcells

用于生成论文全部图表的脚本为：
https://github.com/TansLab/Tans_filamentation/blob/master/ershovwehrensallfigures.m

更具体地，用于加载、（部分分析并）绘制数据的脚本为：
https://github.com/TansLab/Tans_filamentation/blob/master/script20160429_filamentRecoveryDivisionRatioss.m

.mat文件说明

此类.mat文件包含谱系信息，用于生成图1与图2。

表格的每一行对应一个从诞生到分裂的大肠杆菌（Escherichia coli）细胞。

核心字段包括：
P：该细胞的母细胞（编号对应表格中的行号）。
E：该细胞分裂产生的子细胞之一。
D：该细胞分裂产生的另一子细胞。
frame_nrs：该细胞存活对应的成像帧编号。
areapx：以像素为单位的细胞面积。

针对细菌长度的测定采用了不同方法。在四环素（tetracycline）实验中，通常使用`length_fitNew`字段，该值为通过细菌轮廓拟合得到的高阶多项式结果。对于其他应激条件下的实验，则多采用`length_skeleton`字段，该值为细菌骨架的长度，经外推至细菌边缘后得到（之所以采用该方法，是因为此类实验中的细菌常出现难以通过多项式拟合的异常形态）。

细菌的生长率通过对多帧的长度信息拟合指数曲线得到。由于生长率存在波动，部分细菌在若干帧内的生长速度相对较快或较慢，因此拟合时使用的帧数可灵活调整。生长率信息可参考以下字段：`muP15_fitNew_all`、`muP9_skeleton_all`、`muP5_skeleton_all`等。其中，`mu`代表生长率，`PX`表示拟合时采用了目标帧周围X帧的数据，`fitNew_all`与`skeleton_all`分别对应拟合时使用的长度参数类型。

需注意，细胞的诞生尺寸、分裂间期时长以及新增长度，均可通过上述数据结构结合相关参数计算得到（详见对应脚本）。

该数据集还包含更多与长度、尺寸相关的字段，以及荧光数据字段，但后者与本数据集关联不大。

更多信息请参阅论文的方法部分。

数据集详细信息

SulA应激条件数据集：
| 数据文件路径 | 从应激切换至无应激条件的转换时间（分钟） |
| --- | --- |
| `2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTGpos1cropdatapos1crop-Schnitz.mat` | 0 |
| `2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTGpos2cropdatapos2crop-Schnitz.mat` | 0 |
| `2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTGpos3cropdatapos3crop-Schnitz.mat` | 0 |
| `2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTGpos4cropdatapos4crop-Schnitz.mat` | 0 |
| `2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTGpos7cropdatapos7crop-Schnitz.mat` | 0 |
若转换时间为0，则表示成像起始时刻即为应激转换节点。

温度应激条件数据集：
| 数据文件路径 | 从应激切换至无应激条件的转换时间（分钟） |
| --- | --- |
| `2016-03-23_FilaRecovery_asc777_42Cpos4cropdatapos4crop-Schnitz.mat` | 450 |
| `2016-04-07_FilaRecovery_asc777pos2cropdatapos2crop-Schnitz.mat` | 329 |

Delta min四环素应激条件数据集：
| 数据文件路径 | 从应激切换至无应激条件的转换时间（分钟） |
| --- | --- |
| `2017-09-22_FilaRecovery_asc1035_DeltaMinCDEpos1cropbdatapos1cropb-Schnitz.mat` | 5 |
| `2017-09-22_FilaRecovery_asc1035_DeltaMinCDEpos2cropadatapos2cropa-Schnitz.mat` | 5 |
| `2017-09-22_FilaRecovery_asc1035_DeltaMinCDEpos2cropbdatapos2cropb-Schnitz.mat` | 5 |
| `2017-09-22_FilaRecovery_asc1035_DeltaMinCDEpos2cropcdatapos2cropc-Schnitz.mat` | 5 |
| `2017-09-22_FilaRecovery_asc1035_DeltaMinCDEpos3cropadatapos3cropa-Schnitz.mat` | 5 |

四环素数据集1
本次研究仅使用了第1至5组数据集：
| 数据文件路径 | 从应激切换至无应激条件的转换时间（分钟） |
| --- | --- |
| `F schijf AmolfBackup_3april2014USE_DIV1uM_pos3_long.mat` | 890.9800 |
| `F schijf AmolfBackup_3april2014USE_DIV1uM_pos4.mat` | 404.7500 |
| `F schijf AmolfBackup_3april2014USE_DIV1uM_pos4_long.mat` | 0 |
| `F schijf AmolfBackup_3april2014USE_DIV1uM_pos5.mat` | 529.7600 |
| `F schijf AmolfBackup_3april2014USE_DIV1uM_pos5_long.mat` | 0 |
| `F schijf AmolfBackup_3april2014USE_DIV2uM_pos2.mat` | NA |
| `F schijf AmolfBackup_3april2014USE_DIV2uM_pos4.mat` | NA |
| `F schijf AmolfBackup_3april2014USE_DIV2uM_pos6.mat` | NA |
| `F schijf AmolfBackup_3april2014USE_DIV10uM_pos1.mat` | NA |
| `F schijf AmolfBackup_3april2014USE_DIV10uM_pos3.mat` | NA |
| `F schijf AmolfBackup_3april2014USE_DIV10uM_pos6_long.mat` | NA |

四环素数据集2（与上述数据集存在冗余）：
| 数据文件路径 | 从应激切换至无应激条件的转换时间（分钟） |
| --- | --- |
| `2013-12-09pos3cropdatapos3crop-Schnitz.mat` | 890.9800 |
| `2013-09-24pos4cropdatapos4crop-Schnitz.mat` | 404.7500 |
| `2013-12-16pos4cropdatapos4crop-Schnitz.mat` | 0 |
| `2013-09-24pos5cropdatapos5crop-Schnitz.mat` | 529.7600 |
| `2013-12-16pos5cropdatapos5crop-Schnitz.mat` | 0 |